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Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome.

Author information

Affiliations

  • 1. Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
      Authors
    • Snijders AM 1
    • Langley SA 1
    • Huang Y 1
    • Karpen GH 1
    • Mao JH 1
    (5 authors)
  • 2. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
      Authors
    • Kim YM 2
    • Brislawn CJ 2
    • Zink EM 2
    • Fansler SJ 2
    • Casey CP 2
    • Jansson JK 2
    • Metz TO 2
    (7 authors)
  • 3. Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA.
      Authors
    • Noecker C 3
    • Borenstein E 3
    (2 authors)
  • 4. Systems Genetics Core Facility, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
      Authors
    • Miller DR 4
    (1 author)
  • 5. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
      Authors
    • Celniker SE 5
    • Brown JB 5
    (2 authors)

ORCIDs linked to this article

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Nature Microbiology, 28 Nov 2016, 2:16221
https://doi.org/10.1038/nmicrobiol.2016.221 PMID: 27892936 

Abstract 

Although the gut microbiome plays important roles in host physiology, health and disease1, we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system2 to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism. Quantitative trait analysis identified mouse genetic trait loci (QTL) that impact the abundances of specific microbes. Human orthologues of genes in the mouse QTL are implicated in gastrointestinal cancer. Additionally, genes located in mouse QTL for Lactobacillales abundance are implicated in arthritis, rheumatic disease and diabetes. Furthermore, Lactobacillales abundance was predictive of higher host T-helper cell counts, suggesting an important link between Lactobacillales and host adaptive immunity.

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Read article at publisher's site: https://doi.org/10.1038/nmicrobiol.2016.221

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Funding 

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NCCIH NIH HHS (1)